Harvard Condensed Matter Theory Seminars
We present a novel topological classification of RNA secondary
structures with pseudoknots. It is based on the topological genus of
the circular diagram associated to the RNA base-pair structure. The
genus is a positive integer number, whose value quantifies the
topological complexity of the folded RNA structure. In such a
representation, planar diagrams correspond to pure RNA secondary
structures and have zero genus, whereas non planar diagrams correspond
to pseudoknotted structures and have higher genus. We analyze real RNA
structures from the databases wwPDB and Pseudobase, and classify them
according to their topological genus. We compare the results of our
statistical survey with existing theoretical and numerical models. We
also discuss possible applications of this classification and show how
it can be used for identifying new RNA structural motifs.
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